1. Does shield mitigation affect damage done to the hull (once shields are gone or because of shield negation)?
2. If yes, is damage done on a successful shield negation still affected by shield mitigation?
If the answers to these questions are yes and no, respectively, then I think that the shield negation actually makes phase missiles worse in almost all situations (the exception being super shield tanks). The reason being that splitting damage between hull and shield from the beginning allows both to be regenerating from the start of the battle, increaasing the amount of damage the target can take overall. It's possible that a shield tank could have so many more shield hps that the shield negation could take the hull to zero before the shield was gone, potentially overcoming the inadvertant boost to the target, but I think that's probably rare, especially against the AI. I just played a game where I was using phase missiles exclusively, and, with full shield negation (30%) I didn't see a single target die with shield hps left, not even close. I tracked probably 30-40 targets, all factions, capital and frigate (though I'm sure there are a number of ship types I didn't see).
Does anybody want to do the math to figure out how much more shield a target has to have (taking regeneration into account) before shield negation actually helps the Vasari rather than hurting them (assuming the two initial assumptions regarding shield mitigation are correct)? Because I strongly suspect that its a number so high as to be extremely rare, especially in single player.